Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014011.1 Kokia drynarioides strain JFW-HI SEQ_129042, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3876
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.30
Warning! 88 characters in sequence are not A, C, G, or T
Found at i:455 original size:153 final size:153
Alignment explanation
Indices: 163--491 Score: 541
Period size: 153 Copynumber: 2.2 Consensus size: 153
153 TAAAATGGTT
* * *
163 AGCTTCATGATTAGATACTGAAAGGTGGACCAAATTCGTCTTCCTGATGAAATACAGAGAACCGA
1 AGCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAAATACAGAGAACCGA
*
228 ATTGATACAAGTGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCGAGGCTCA
66 ATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCGAGGCTCA
*
293 ATGCAAGCAAATCTTCGAACCCT
131 ATGCAAGCAAATCTTCGAACCCC
* * *
316 ATCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGA
1 AGCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAAATACAGAGAACCGA
* * * *
381 ATTGAAACAAGTGAGGTGGTCATGTTCTTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCA
66 ATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCGAGGCTCA
*
446 ATGCGAGCAAATCTTCGAACCCC
131 ATGCAAGCAAATCTTCGAACCCC
469 AGCTTCCTGATGAGATACTGAGA
1 AGCTTCCTGATGAGATACTGAGA
492 AGCAGGTCAA
Statistics
Matches: 162, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 162 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (153 bp):
AGCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAAATACAGAGAACCGA
ATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCGAGGCTCA
ATGCAAGCAAATCTTCGAACCCC
Found at i:666 original size:201 final size:201
Alignment explanation
Indices: 318--836 Score: 817
Period size: 201 Copynumber: 2.6 Consensus size: 201
308 CGAACCCTAT
318 CTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
* * *
383 TGAAACAAGTGAGGTGGTCATGTTCTTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAAT
66 TGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAAT
* * *
448 GCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAT
131 GCGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAACCAATAAAAT
513 GGTTAG
196 GGTTAG
*
519 CTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
*
584 TGAAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCGAGGCTCAAT
66 TGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAAT
* * *
649 GCGAGAAAATGTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCGAACCAATAAAGT
131 GCGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAACCAATAAAAT
714 GGTTAG
196 GGTTAG
* * * * *
720 CTTCCTGATGAGATA-TGGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGGGAAGCGGA
1 CTTCCTGATGAGATACT-GAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAA
** * * *
784 TTGAAACAAACGATGCGGTCATCTTCCTGATAAGATACTA-AGAAGTAAACCAA
65 TTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATAC-AGAGAAGTATACCAA
837 ATCAACGACA
Statistics
Matches: 293, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
200 1 0.00
201 291 0.99
202 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (201 bp):
CTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGAAT
TGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTCAAT
GCGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAACAGGTCAAACCAATAAAAT
GGTTAG
Found at i:1193 original size:6 final size:6
Alignment explanation
Indices: 1184--1270 Score: 81
Period size: 6 Copynumber: 14.8 Consensus size: 6
1174 GATTTATTTC
* * **
1184 TAAATT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** *
1231 TAAATT T-GTTT TAAATT TAAATT T-AGTT TAAATT TGAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAAT
1271 ATTTTTAAAA
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
5 11 0.17
6 48 0.76
7 4 0.06
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (6 bp):
TAAATT
Found at i:1206 original size:17 final size:17
Alignment explanation
Indices: 1170--1270 Score: 76
Period size: 17 Copynumber: 5.4 Consensus size: 17
1160 TTTAAATTAT
* *
1170 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTT-TAAA
1188 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
1205 TTTAAATTTAAATTCATTTTTAAA
1 TTTAAATTT--A--C---TTTAAA
**
1229 TTTAAATTTGTTTTAAA
1 TTTAAATTTACTTTAAA
*
1246 TTTAAATTTAGTTTAAA
1 TTTAAATTTACTTTAAA
1263 TTTGAAAT
1 TTT-AAAT
1271 ATTTTTAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
17 37 0.54
18 15 0.22
19 1 0.01
21 1 0.01
24 15 0.22
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:1229 original size:41 final size:41
Alignment explanation
Indices: 1170--1255 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
1160 TTTAAATTAT
* *
1170 TTTAGATTTATTTCTAAATTTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
* **
1211 TTTAAATTCATTTTTAAATTTAAATTTGTTTTAAATTTAAA
1 TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
1252 TTTA
1 TTTA
1256 GTTTAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAATTTAAATTTACTTTAAATTTAAA
Found at i:1277 original size:17 final size:16
Alignment explanation
Indices: 1205--1279 Score: 80
Period size: 17 Copynumber: 4.4 Consensus size: 16
1195 TTACTTTAAA
1205 TTTAAATTTAAATTCATT
1 TTTAAATTTAAA-T-ATT
*
1223 TTTAAATTTAAATTTGT
1 TTTAAATTTAAATAT-T
1240 TTTAAATTTAAAT-TT
1 TTTAAATTTAAATATT
1255 AGTTTAAATTTGAAATATT
1 --TTTAAATTT-AAATATT
1274 TTTAAA
1 TTTAAA
1280 ACTTAAACTT
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
15 1 0.02
16 2 0.04
17 30 0.59
18 16 0.31
19 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (16 bp):
TTTAAATTTAAATATT
Found at i:3148 original size:88 final size:86
Alignment explanation
Indices: 3030--3497 Score: 416
Period size: 88 Copynumber: 5.3 Consensus size: 86
3020 CCCTAGAGGT
3030 CCCTAAACTGTCCAAAAATT--ATGTTTTGACCTTCGAACTTCCAAAAATTCCATTTTGACCTCG
1 CCCTAAACT-TCCAAAAATTCCAT-TTTT-ACC-TCGAACTTCCAAAAATTCCATTTTGACCTCG
3093 AAACTTCCAAAAATTACATTTTTAC
62 AAACTTCCAAAAATTACATTTTTAC
* * *
3118 CCCTAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCCG-
1 CCCTAAACTTCCAAAAATTCCATTTTT-ACCTCG-AACTTCCAAAAATTCCATTTTGA-CCTCGA
* *
3182 AACTTCTAAAAATTCCATTTTTAAC
63 AACTTCCAAAAATTACATTTTT-AC
* * * * *
3207 CCTTAAACTTCCAAAAATTACATTTCTACC-CATGAACTTCCAAAAATTCCATTTTTAACC-CTA
1 CCCTAAACTTCCAAAAATTCCATTTTTACCTC--GAACTTCCAAAAATTCCA-TTTTGACCTC-G
*
3270 AAACTTTCAAAAATTACATTTTTAC
62 AAACTTCCAAAAATTACATTTTTAC
** * ** * * *
3295 CCCCGAACTTCCAAAAATTCCATTTTAACCTTAAAACTTCTAAAAATTACATATTT-ACCCTTG-
1 CCCTAAACTTCCAAAAATTCCATTTTTACC-TCGAACTTCCAAAAATTCCAT-TTTGA-CCTCGA
3358 AACTTCCAAAAATT-CTATTTTTGAC
63 AACTTCCAAAAATTAC-ATTTTT-AC
* *** * * * * *
3383 CCCAAAACTTTTGAAAATTACATTTTTACCCCCAACTTCCAAAAACTCCATTTTTGACCTCTAAA
1 CCCTAAACTTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTCCA-TTTTGACCTCGAAA
*
3448 CTTTCAAAAATTACCA-TTTTAC
65 CTTCCAAAAATTA-CATTTTTAC
*
3470 CCCTGAA-TGTCCAAAAATTCCATTTTTA
1 CCCTAAACT-TCCAAAAATTCCATTTTTA
3498 ATCTCGATTT
Statistics
Matches: 308, Mismatches: 49, Indels: 47
0.76 0.12 0.12
Matches are distributed among these distances:
86 2 0.01
87 78 0.25
88 169 0.55
89 58 0.19
90 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (86 bp):
CCCTAAACTTCCAAAAATTCCATTTTTACCTCGAACTTCCAAAAATTCCATTTTGACCTCGAAAC
TTCCAAAAATTACATTTTTAC
Found at i:3154 original size:59 final size:59
Alignment explanation
Indices: 3064--3496 Score: 547
Period size: 59 Copynumber: 7.4 Consensus size: 59
3054 TTTGACCTTC
*
3064 GAACTTCCAAAAATTCCA-TTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCT
1 GAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACATTTTTACCCCT
* * *
3122 AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCC
1 GAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACATTTTTACCCCT
* * * * *
3181 GAACTTCTAAAAATTCCATTTTTAACC-CTTAAACTTCCAAAAATTACATTTCTACCCAT
1 GAACTTCCAAAAATTCCATTTTTGACCTC-AAAACTTCCAAAAATTACATTTTTACCCCT
* * *
3240 GAACTTCCAAAAATTCCATTTTTAACC-CTAAAACTTTCAAAAATTACATTTTTACCCCC
1 GAACTTCCAAAAATTCCATTTTTGACCTC-AAAACTTCCAAAAATTACATTTTTACCCCT
* * * * *
3299 GAACTTCCAAAAATTCCA-TTTTAACCTTAAAACTTCTAAAAATTACATATTTACCCTT
1 GAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACATTTTTACCCCT
* * ***
3357 GAACTTCCAAAAATTCTATTTTTGACCCCAAAACTTTTGAAAATTACATTTTTACCCC-
1 GAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACATTTTTACCCCT
* * * *
3415 CAACTTCCAAAAACTCCATTTTTGACCTCTAAACTTTCAAAAATTACCA-TTTTACCCCT
1 GAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTA-CATTTTTACCCCT
3474 GAA-TGTCCAAAAATTCCATTTTT
1 GAACT-TCCAAAAATTCCATTTTT
3497 AATCTCGATT
Statistics
Matches: 330, Mismatches: 38, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
58 117 0.35
59 213 0.65
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (59 bp):
GAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATTACATTTTTACCCCT
Found at i:3390 original size:117 final size:116
Alignment explanation
Indices: 3063--3496 Score: 597
Period size: 117 Copynumber: 3.7 Consensus size: 116
3053 TTTTGACCTT
* * *
3063 CGAACTTCCAAAAATTCCA-TTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCCTAAACT
1 CGAACTTCCAAAAATTCCATTTTTAACCT-TAAACTTCCAAAAATTACA-TTTTACCCCTGAACT
* * *
3127 TCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTACATTTTTACCCC
64 TCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCC
* *
3180 CGAACTTCTAAAAATTCCATTTTTAACCCTTAAACTTCCAAAAATTACATTTCTACCCATGAACT
1 CGAACTTCCAAAAATTCCATTTTTAA-CCTTAAACTTCCAAAAATTACATTT-TACCCCTGAACT
* *
3245 TCCAAAAATTCCATTTTTAACCCTAAAACTTTCAAAAATTACATTTTTACCCC
64 TCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCC
* *
3298 CGAACTTCCAAAAATTCCA-TTTTAACCTTAAAACTTCTAAAAATTACATATTTACCCTTGAACT
1 CGAACTTCCAAAAATTCCATTTTTAACCTT-AAACTTCCAAAAATTACAT-TTTACCCCTGAACT
* **
3362 TCCAAAAATTCTATTTTTGACCCCAAAACTTTTGAAAATTACATTTTTACCCC
64 TCCAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCC
* * *
3415 C-AACTTCCAAAAACTCCATTTTTGACCTCTAAACTTTCAAAAATTACCATTTTACCCCTGAA-T
1 CGAACTTCCAAAAATTCCATTTTTAACCT-TAAACTTCCAAAAATTA-CATTTTACCCCTGAACT
3478 GTCCAAAAATTCCATTTTT
64 -TCCAAAAATTCCATTTTT
3497 AATCTCGATT
Statistics
Matches: 284, Mismatches: 24, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
116 21 0.07
117 155 0.55
118 105 0.37
119 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (116 bp):
CGAACTTCCAAAAATTCCATTTTTAACCTTAAACTTCCAAAAATTACATTTTACCCCTGAACTTC
CAAAAATTCCATTTTTGACCCCAAAACTTTCAAAAATTACATTTTTACCCC
Found at i:3496 original size:29 final size:29
Alignment explanation
Indices: 3064--3497 Score: 403
Period size: 29 Copynumber: 14.8 Consensus size: 29
3054 TTTGACCTTC
* *
3064 GAACTTCCAAAAATTCCATTTTGACCTC-
1 GAACTTCCAAAAATTCCATTTTTACCCCT
*
3092 GAAACTTCCAAAAATTACATTTTTACCCCT
1 G-AACTTCCAAAAATTCCATTTTTACCCCT
* *
3122 AAACTTCCAAAAATTCCATTTTTGACCTC-
1 GAACTTCCAAAAATTCCATTTTT-ACCCCT
* *
3151 GAAACTTCCAAAAATTACATTTTTACCCCC
1 G-AACTTCCAAAAATTCCATTTTTACCCCT
* *
3181 GAACTTCTAAAAATTCCATTTTTAACCCTT
1 GAACTTCCAAAAATTCCATTTTT-ACCCCT
* * * *
3211 AAACTTCCAAAAATTACATTTCTACCCAT
1 GAACTTCCAAAAATTCCATTTTTACCCCT
*
3240 GAACTTCCAAAAATTCCATTTTTAACCCT
1 GAACTTCCAAAAATTCCATTTTTACCCCT
* * * *
3269 AAAACTTTCAAAAATTACATTTTTACCCCC
1 -GAACTTCCAAAAATTCCATTTTTACCCCT
* *
3299 GAACTTCCAAAAATTCCA-TTTTAACCTT
1 GAACTTCCAAAAATTCCATTTTTACCCCT
* * * * *
3327 AAAACTTCTAAAAATTACATATTTACCCTT
1 -GAACTTCCAAAAATTCCATTTTTACCCCT
* *
3357 GAACTTCCAAAAATTCTATTTTTGACCCCA
1 GAACTTCCAAAAATTCCATTTTT-ACCCCT
* *** *
3387 AAACTTTTGAAAATTACATTTTTACCCC-
1 GAACTTCCAAAAATTCCATTTTTACCCCT
* * *
3415 CAACTTCCAAAAACTCCATTTTTGACCTCT
1 GAACTTCCAAAAATTCCATTTTT-ACCCCT
* *
3445 AAACTTTCAAAAATTACCA-TTTTACCCCT
1 GAACTTCCAAAAATT-CCATTTTTACCCCT
3474 GAA-TGTCCAAAAATTCCATTTTTA
1 GAACT-TCCAAAAATTCCATTTTTA
3498 ATCTCGATTT
Statistics
Matches: 326, Mismatches: 65, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
28 29 0.09
29 176 0.54
30 118 0.36
31 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
GAACTTCCAAAAATTCCATTTTTACCCCT
Found at i:3566 original size:58 final size:58
Alignment explanation
Indices: 3097--3602 Score: 273
Period size: 59 Copynumber: 8.7 Consensus size: 58
3087 ACCTCGAAAC
* * * *
3097 TTCCAAAAATTA-CATTTTTACCCCTAAACT-TCCAAAAATTCCATTTTTGACCTCGAAA-C
1 TTCCAAAAATTACCA-TTTTACCCCTGAA-TATCCAAAAATTCAATTTTTAACCT--AAATT
* * * *
3156 TTCCAAAAATTA-CATTTTTACCCCCGAACT-TCTAAAAATTCCATTTTTAACCCTTAAA-C
1 TTCCAAAAATTACCA-TTTTACCCCTGAA-TATCCAAAAATTCAATTTTTAA-CC-TAAATT
* * *
3215 TTCCAAAAATTA-CATTTCTACCCATGAACT-TCCAAAAATTCCATTTTTAACCCTAAAACT
1 TTCCAAAAATTACCATTT-TACCCCTGAA-TATCCAAAAATTCAATTTTTAA-CCT-AAATT
* * **
3275 TT-CAAAAATTA-CATTTTTACCCCCGAACT-TCCAAAAATTCCA-TTTTAACCTTAAAAC
1 TTCCAAAAATTACCA-TTTTACCCCTGAA-TATCCAAAAATTCAATTTTTAACC-TAAATT
* * * * *
3332 TTCTAAAAATTA-CATATTTACCCTTGAACT-TCCAAAAATTCTATTTTTGACCCCAAAACTT
1 TTCCAAAAATTACCAT-TTTACCCCTGAA-TATCCAAAAATTCAATTTTT-A-ACCTAAA-TT
* * * * * *
3393 TT--GAAAATTA-CATTTTTACCCC-CAACT-TCCAAAAACTCCATTTTTGACCTCTAAACT
1 TTCCAAAAATTACCA-TTTTACCCCTGAA-TATCCAAAAATTCAATTTTT-AAC-CTAAATT
* * * **
3450 TT-CAAAAATTACCATTTTACCCCTGAATGTCCAAAAATTCCATTTTTAATCTCGATT
1 TTCCAAAAATTACCATTTTACCCCTGAATATCCAAAAATTCAATTTTTAACCTAAATT
** * * * *
3507 TTTTAAAAATTACCGTTTTACCCCTGGATAT-CTAAAATTTAATTTTTAACCCTAAATT
1 TTCCAAAAATTACCATTTTACCCCTGAATATCCAAAAATTCAATTTTTAA-CCTAAATT
* *
3565 TTCCCAAAATTACCATTTTA-CCCTCGAGTATCCAAAAA
1 TTCCAAAAATTACCATTTTACCCCT-GAATATCCAAAAA
3603 GTTTCATTTT
Statistics
Matches: 372, Mismatches: 52, Indels: 46
0.79 0.11 0.10
Matches are distributed among these distances:
57 38 0.10
58 138 0.37
59 179 0.48
60 12 0.03
61 5 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
TTCCAAAAATTACCATTTTACCCCTGAATATCCAAAAATTCAATTTTTAACCTAAATT
Found at i:3602 original size:29 final size:29
Alignment explanation
Indices: 3452--3602 Score: 78
Period size: 29 Copynumber: 5.2 Consensus size: 29
3442 TCTAAACTTT
* *
3452 CAAAAATTACCATTTTACCC-CTGAATGTC
1 CAAAAATTACCATTTTACCCTC-GATTATC
** * *
3481 CAAAAATT-CCATTTTTAATCTCGATTTTT
1 CAAAAATTACCA-TTTTACCCTCGATTATC
* * *
3510 TAAAAATTACCGTTTTACCCCTGGA-TATC
1 CAAAAATTACCATTTTA-CCCTCGATTATC
* * ** *
3539 TAAAATTTA--ATTTTTAACCCTAAATTTTC
1 CAAAAATTACCA-TTTT-ACCCTCGATTATC
* *
3568 CCAAAATTACCATTTTACCCTCGAGTATC
1 CAAAAATTACCATTTTACCCTCGATTATC
3597 CAAAAA
1 CAAAAA
3603 GTTTCATTTT
Statistics
Matches: 88, Mismatches: 25, Indels: 18
0.67 0.19 0.14
Matches are distributed among these distances:
28 12 0.14
29 64 0.73
30 11 0.12
31 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCGATTATC
Done.